[gmx-users] potential energy of only the protein

[Mark Abraham]

sarbani chattopadhyay wrote:
>  
> hi,
>   I want to get the potential energy of only the protein ie. without 
> that of the
> water.'g_energy' calculates the energy from the energy file. The groups 
> written for the
> "energygroups" are 'protein sol'.
> Is there any way to get the energy only of the protein?

I concur with David's warnings and suggestions.

In particular, g_energy will let you deduce the non-bonded component of 
the protein-protein interactions if you run it and see what it lets you 
choose. Extracting the bonded component is more involved, requiring a 
tpbconv to get out just the protein, a trjconv to get out just the 
protein, and then an mdrun -rerun on those subsets. Then, these numbers 
aren't going to tell you anything useful that I know of.

Mark